# | Line 36 | Line 36 | |
---|---|---|
36 | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | |
37 | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | |
38 | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | |
39 | < | * [4] Vardeman & Gezelter, in progress (2009). |
39 | > | * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 | > | * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 | */ | |
42 | ||
43 | #define _LARGEFILE_SOURCE64 | |
# | Line 57 | Line 58 | |
58 | #include "utils/simError.h" | |
59 | #include "utils/MemoryUtils.hpp" | |
60 | #include "utils/StringTokenizer.hpp" | |
61 | + | #include "brains/Thermo.hpp" |
62 | ||
63 | #ifdef IS_MPI | |
62 | – | |
64 | #include <mpi.h> | |
65 | < | #define TAKE_THIS_TAG_CHAR 0 |
65 | < | #define TAKE_THIS_TAG_INT 1 |
65 | > | #endif |
66 | ||
67 | – | #endif // is_mpi |
67 | ||
69 | – | |
68 | namespace OpenMD { | |
69 | ||
70 | DumpReader::DumpReader(SimInfo* info, const std::string& filename) | |
# | Line 142 | Line 140 | namespace OpenMD { | |
140 | prevPos = currPos; | |
141 | bool foundOpenSnapshotTag = false; | |
142 | bool foundClosedSnapshotTag = false; | |
143 | + | bool foundOpenSiteDataTag = false; |
144 | while(inFile_->getline(buffer, bufferSize)) { | |
145 | ++lineNo; | |
146 | ||
# | Line 243 | Line 242 | namespace OpenMD { | |
242 | ||
243 | if (needCOMprops_) { | |
244 | Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); | |
245 | + | Thermo thermo(info_); |
246 | Vector3d com; | |
247 | – | Vector3d comvel; |
248 | – | Vector3d comw; |
249 | – | if (needPos_ && needVel_){ |
250 | – | info_->getComAll(com, comvel); |
251 | – | comw = info_->getAngularMomentum(); |
252 | – | }else{ |
253 | – | com = info_->getCom(); |
254 | – | comvel = 0.0; |
255 | – | comw = 0.0; |
256 | – | } |
257 | – | s->setCOMprops(com, comvel, comw); |
258 | – | } |
247 | ||
248 | + | if (needPos_ && needVel_) { |
249 | + | Vector3d comvel; |
250 | + | Vector3d comw; |
251 | + | thermo.getComAll(com, comvel); |
252 | + | comw = thermo.getAngularMomentum(); |
253 | + | } else { |
254 | + | com = thermo.getCom(); |
255 | + | } |
256 | + | } |
257 | } | |
258 | ||
259 | void DumpReader::readSet(int whichFrame) { | |
# | Line 324 | Line 321 | namespace OpenMD { | |
321 | ||
322 | inputStream.getline(buffer, bufferSize); | |
323 | line = buffer; | |
324 | < | if (line.find("</Snapshot>") == std::string::npos) { |
325 | < | sprintf(painCave.errMsg, |
326 | < | "DumpReader Error: can not find </Snapshot>\n"); |
327 | < | painCave.isFatal = 1; |
328 | < | simError(); |
329 | < | } |
330 | < | |
324 | > | |
325 | > | if (line.find("<SiteData>") != std::string::npos) { |
326 | > | //read SiteData |
327 | > | readSiteData(inputStream); |
328 | > | } else { |
329 | > | if (line.find("</Snapshot>") == std::string::npos) { |
330 | > | sprintf(painCave.errMsg, |
331 | > | "DumpReader Error: can not find </Snapshot>\n"); |
332 | > | painCave.isFatal = 1; |
333 | > | simError(); |
334 | > | } |
335 | > | } |
336 | } | |
337 | ||
338 | void DumpReader::parseDumpLine(const std::string& line) { | |
# | Line 473 | Line 475 | namespace OpenMD { | |
475 | integrableObject->setParticlePot(particlePot); | |
476 | break; | |
477 | } | |
478 | + | case 'c' : { |
479 | + | |
480 | + | RealType flucQPos; |
481 | + | flucQPos = tokenizer.nextTokenAsDouble(); |
482 | + | integrableObject->setFlucQPos(flucQPos); |
483 | + | break; |
484 | + | } |
485 | + | case 'w' : { |
486 | + | |
487 | + | RealType flucQVel; |
488 | + | flucQVel = tokenizer.nextTokenAsDouble(); |
489 | + | integrableObject->setFlucQVel(flucQVel); |
490 | + | break; |
491 | + | } |
492 | + | case 'g' : { |
493 | + | |
494 | + | RealType flucQFrc; |
495 | + | flucQFrc = tokenizer.nextTokenAsDouble(); |
496 | + | integrableObject->setFlucQFrc(flucQFrc); |
497 | + | break; |
498 | + | } |
499 | + | case 'e' : { |
500 | + | |
501 | + | Vector3d eField; |
502 | + | eField[0] = tokenizer.nextTokenAsDouble(); |
503 | + | eField[1] = tokenizer.nextTokenAsDouble(); |
504 | + | eField[2] = tokenizer.nextTokenAsDouble(); |
505 | + | integrableObject->setElectricField(eField); |
506 | + | break; |
507 | + | } |
508 | default: { | |
509 | sprintf(painCave.errMsg, | |
510 | "DumpReader Error: %s is an unrecognized type\n", type.c_str()); | |
# | Line 487 | Line 519 | namespace OpenMD { | |
519 | } | |
520 | ||
521 | ||
522 | < | void DumpReader::readStuntDoubles(std::istream& inputStream) { |
522 | > | void DumpReader::parseSiteLine(const std::string& line) { |
523 | ||
524 | + | StringTokenizer tokenizer(line); |
525 | + | int nTokens; |
526 | + | |
527 | + | nTokens = tokenizer.countTokens(); |
528 | + | |
529 | + | if (nTokens < 2) { |
530 | + | sprintf(painCave.errMsg, |
531 | + | "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
532 | + | painCave.isFatal = 1; |
533 | + | simError(); |
534 | + | } |
535 | + | |
536 | + | /** |
537 | + | * The first token is the global integrable object index. |
538 | + | */ |
539 | + | |
540 | + | int index = tokenizer.nextTokenAsInt(); |
541 | + | StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
542 | + | if (integrableObject == NULL) { |
543 | + | return; |
544 | + | } |
545 | + | StuntDouble* sd = integrableObject; |
546 | + | |
547 | + | /** |
548 | + | * Test to see if the next token is an integer or not. If not, |
549 | + | * we've got data on the integrable object itself. If there is an |
550 | + | * integer, we're parsing data for a site on a rigid body. |
551 | + | */ |
552 | + | |
553 | + | std::string indexTest = tokenizer.peekNextToken(); |
554 | + | std::istringstream i(indexTest); |
555 | + | int siteIndex; |
556 | + | if (i >> siteIndex) { |
557 | + | // chew up this token and parse as an int: |
558 | + | siteIndex = tokenizer.nextTokenAsInt(); |
559 | + | RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
560 | + | sd = rb->getAtoms()[siteIndex]; |
561 | + | } |
562 | + | |
563 | + | /** |
564 | + | * The next token contains information on what follows. |
565 | + | */ |
566 | + | std::string type = tokenizer.nextToken(); |
567 | + | int size = type.size(); |
568 | + | |
569 | + | for(int i = 0; i < size; ++i) { |
570 | + | switch(type[i]) { |
571 | + | |
572 | + | case 'u' : { |
573 | + | |
574 | + | RealType particlePot; |
575 | + | particlePot = tokenizer.nextTokenAsDouble(); |
576 | + | sd->setParticlePot(particlePot); |
577 | + | break; |
578 | + | } |
579 | + | case 'c' : { |
580 | + | |
581 | + | RealType flucQPos; |
582 | + | flucQPos = tokenizer.nextTokenAsDouble(); |
583 | + | sd->setFlucQPos(flucQPos); |
584 | + | break; |
585 | + | } |
586 | + | case 'w' : { |
587 | + | |
588 | + | RealType flucQVel; |
589 | + | flucQVel = tokenizer.nextTokenAsDouble(); |
590 | + | sd->setFlucQVel(flucQVel); |
591 | + | break; |
592 | + | } |
593 | + | case 'g' : { |
594 | + | |
595 | + | RealType flucQFrc; |
596 | + | flucQFrc = tokenizer.nextTokenAsDouble(); |
597 | + | sd->setFlucQFrc(flucQFrc); |
598 | + | break; |
599 | + | } |
600 | + | case 'e' : { |
601 | + | |
602 | + | Vector3d eField; |
603 | + | eField[0] = tokenizer.nextTokenAsDouble(); |
604 | + | eField[1] = tokenizer.nextTokenAsDouble(); |
605 | + | eField[2] = tokenizer.nextTokenAsDouble(); |
606 | + | sd->setElectricField(eField); |
607 | + | break; |
608 | + | } |
609 | + | default: { |
610 | + | sprintf(painCave.errMsg, |
611 | + | "DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
612 | + | painCave.isFatal = 1; |
613 | + | simError(); |
614 | + | break; |
615 | + | } |
616 | + | } |
617 | + | } |
618 | + | } |
619 | + | |
620 | + | |
621 | + | void DumpReader::readStuntDoubles(std::istream& inputStream) { |
622 | + | |
623 | inputStream.getline(buffer, bufferSize); | |
624 | std::string line(buffer); | |
625 | ||
# | Line 511 | Line 642 | namespace OpenMD { | |
642 | ||
643 | } | |
644 | ||
645 | + | void DumpReader::readSiteData(std::istream& inputStream) { |
646 | + | |
647 | + | inputStream.getline(buffer, bufferSize); |
648 | + | std::string line(buffer); |
649 | + | |
650 | + | if (line.find("<SiteData>") == std::string::npos) { |
651 | + | // site data isn't required for a simulation, so skip |
652 | + | return; |
653 | + | } |
654 | + | |
655 | + | while(inputStream.getline(buffer, bufferSize)) { |
656 | + | line = buffer; |
657 | + | |
658 | + | if(line.find("</SiteData>") != std::string::npos) { |
659 | + | break; |
660 | + | } |
661 | + | |
662 | + | parseSiteLine(line); |
663 | + | } |
664 | + | |
665 | + | } |
666 | + | |
667 | void DumpReader::readFrameProperties(std::istream& inputStream) { | |
668 | ||
669 | Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); | |
# | Line 556 | Line 709 | namespace OpenMD { | |
709 | hmat(2, 2) = tokenizer.nextTokenAsDouble(); | |
710 | s->setHmat(hmat); | |
711 | } else if (propertyName == "Thermostat") { | |
712 | < | RealType chi = tokenizer.nextTokenAsDouble(); |
713 | < | RealType integralOfChiDt = tokenizer.nextTokenAsDouble(); |
714 | < | s->setChi(chi); |
715 | < | s->setIntegralOfChiDt(integralOfChiDt); |
712 | > | pair<RealType, RealType> thermostat; |
713 | > | thermostat.first = tokenizer.nextTokenAsDouble(); |
714 | > | thermostat.second = tokenizer.nextTokenAsDouble(); |
715 | > | s->setThermostat(thermostat); |
716 | } else if (propertyName == "Barostat") { | |
717 | Mat3x3d eta; | |
718 | eta(0, 0) = tokenizer.nextTokenAsDouble(); | |
# | Line 571 | Line 724 | namespace OpenMD { | |
724 | eta(2, 0) = tokenizer.nextTokenAsDouble(); | |
725 | eta(2, 1) = tokenizer.nextTokenAsDouble(); | |
726 | eta(2, 2) = tokenizer.nextTokenAsDouble(); | |
727 | < | s->setEta(eta); |
727 | > | s->setBarostat(eta); |
728 | } else { | |
729 | sprintf(painCave.errMsg, | |
730 | "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
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+ | Added lines |
< | Changed lines |
> | Changed lines |